ID   CLSY2_ARATH             Reviewed;        1261 AA.
AC   F4K493;
DT   18-SEP-2013, integrated into UniProtKB/Swiss-Prot.
DT   28-JUN-2011, sequence version 1.
DT   03-AUG-2022, entry version 61.
DE   RecName: Full=SNF2 domain-containing protein CLASSY 2;
DE   AltName: Full=Protein CHROMATIN REMODELING 42;
GN   Name=CLSY2; Synonyms=CHR42; OrderedLocusNames=At5g20420; ORFNames=F7C8.10;
OS   Arabidopsis thaliana (Mouse-ear cress).
OC   Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta;
OC   Spermatophyta; Magnoliopsida; eudicotyledons; Gunneridae; Pentapetalae;
OC   rosids; malvids; Brassicales; Brassicaceae; Camelineae; Arabidopsis.
OX   NCBI_TaxID=3702;
RN   [1]
RP   NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC   STRAIN=cv. Columbia;
RX   PubMed=11130714; DOI=10.1038/35048507;
RA   Tabata S., Kaneko T., Nakamura Y., Kotani H., Kato T., Asamizu E.,
RA   Miyajima N., Sasamoto S., Kimura T., Hosouchi T., Kawashima K., Kohara M.,
RA   Matsumoto M., Matsuno A., Muraki A., Nakayama S., Nakazaki N., Naruo K.,
RA   Okumura S., Shinpo S., Takeuchi C., Wada T., Watanabe A., Yamada M.,
RA   Yasuda M., Sato S., de la Bastide M., Huang E., Spiegel L., Gnoj L.,
RA   O'Shaughnessy A., Preston R., Habermann K., Murray J., Johnson D.,
RA   Rohlfing T., Nelson J., Stoneking T., Pepin K., Spieth J., Sekhon M.,
RA   Armstrong J., Becker M., Belter E., Cordum H., Cordes M., Courtney L.,
RA   Courtney W., Dante M., Du H., Edwards J., Fryman J., Haakensen B.,
RA   Lamar E., Latreille P., Leonard S., Meyer R., Mulvaney E., Ozersky P.,
RA   Riley A., Strowmatt C., Wagner-McPherson C., Wollam A., Yoakum M., Bell M.,
RA   Dedhia N., Parnell L., Shah R., Rodriguez M., Hoon See L., Vil D.,
RA   Baker J., Kirchoff K., Toth K., King L., Bahret A., Miller B., Marra M.A.,
RA   Martienssen R., McCombie W.R., Wilson R.K., Murphy G., Bancroft I.,
RA   Volckaert G., Wambutt R., Duesterhoeft A., Stiekema W., Pohl T.,
RA   Entian K.-D., Terryn N., Hartley N., Bent E., Johnson S., Langham S.-A.,
RA   McCullagh B., Robben J., Grymonprez B., Zimmermann W., Ramsperger U.,
RA   Wedler H., Balke K., Wedler E., Peters S., van Staveren M., Dirkse W.,
RA   Mooijman P., Klein Lankhorst R., Weitzenegger T., Bothe G., Rose M.,
RA   Hauf J., Berneiser S., Hempel S., Feldpausch M., Lamberth S.,
RA   Villarroel R., Gielen J., Ardiles W., Bents O., Lemcke K., Kolesov G.,
RA   Mayer K.F.X., Rudd S., Schoof H., Schueller C., Zaccaria P., Mewes H.-W.,
RA   Bevan M., Fransz P.F.;
RT   "Sequence and analysis of chromosome 5 of the plant Arabidopsis thaliana.";
RL   Nature 408:823-826(2000).
RN   [2]
RP   GENOME REANNOTATION.
RC   STRAIN=cv. Columbia;
RX   PubMed=27862469; DOI=10.1111/tpj.13415;
RA   Cheng C.Y., Krishnakumar V., Chan A.P., Thibaud-Nissen F., Schobel S.,
RA   Town C.D.;
RT   "Araport11: a complete reannotation of the Arabidopsis thaliana reference
RT   genome.";
RL   Plant J. 89:789-804(2017).
RN   [3]
RP   IDENTIFICATION, GENE FAMILY, AND NOMENCLATURE.
RX   PubMed=17526749; DOI=10.1105/tpc.107.051540;
RA   Smith L.M., Pontes O., Searle I., Yelina N., Yousafzai F.K., Herr A.J.,
RA   Pikaard C.S., Baulcombe D.C.;
RT   "An SNF2 protein associated with nuclear RNA silencing and the spread of a
RT   silencing signal between cells in Arabidopsis.";
RL   Plant Cell 19:1507-1521(2007).
RN   [4]
RP   IDENTIFICATION BY MASS SPECTROMETRY, AND INTERACTION WITH NRPD1.
RX   PubMed=21811420; DOI=10.1371/journal.pgen.1002195;
RA   Law J.A., Vashisht A.A., Wohlschlegel J.A., Jacobsen S.E.;
RT   "SHH1, a homeodomain protein required for DNA methylation, as well as RDR2,
RT   RDM4, and chromatin remodeling factors, associate with RNA polymerase IV.";
RL   PLoS Genet. 7:E1002195-E1002195(2011).
RN   [5]
RP   GENE FAMILY.
RX   PubMed=24265739; DOI=10.1371/journal.pone.0078982;
RA   Xu R., Zhang S., Huang J., Zheng C.;
RT   "Genome-wide comparative in silico analysis of the RNA helicase gene family
RT   in Zea mays and Glycine max: a comparison with Arabidopsis and Oryza
RT   sativa.";
RL   PLoS ONE 8:E78982-E78982(2013).
RN   [6]
RP   IDENTIFICATION BY MASS SPECTROMETRY, AND INTERACTION WITH SHH1.
RX   PubMed=23637343; DOI=10.1073/pnas.1300585110;
RA   Zhang H., Ma Z.Y., Zeng L., Tanaka K., Zhang C.J., Ma J., Bai G., Wang P.,
RA   Zhang S.W., Liu Z.W., Cai T., Tang K., Liu R., Shi X., He X.J., Zhu J.K.;
RT   "DTF1 is a core component of RNA-directed DNA methylation and may assist in
RT   the recruitment of Pol IV.";
RL   Proc. Natl. Acad. Sci. U.S.A. 110:8290-8295(2013).
CC   -!- FUNCTION: Probable chromatin remodeling factor.
CC   -!- SUBUNIT: Interacts with NRPD1 and SHH1. {ECO:0000269|PubMed:21811420,
CC       ECO:0000269|PubMed:23637343}.
CC   -!- SUBCELLULAR LOCATION: Nucleus {ECO:0000250}.
CC   -!- SIMILARITY: Belongs to the helicase family. {ECO:0000305}.
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DR   EMBL; AF296833; -; NOT_ANNOTATED_CDS; Genomic_DNA.
DR   EMBL; CP002688; AED92841.1; -; Genomic_DNA.
DR   RefSeq; NP_197542.1; NM_122049.3.
DR   AlphaFoldDB; F4K493; -.
DR   BioGRID; 17440; 2.
DR   STRING; 3702.AT5G20420.1; -.
DR   PaxDb; F4K493; -.
DR   PRIDE; F4K493; -.
DR   ProteomicsDB; 240893; -.
DR   EnsemblPlants; AT5G20420.1; AT5G20420.1; AT5G20420.
DR   GeneID; 832164; -.
DR   Gramene; AT5G20420.1; AT5G20420.1; AT5G20420.
DR   KEGG; ath:AT5G20420; -.
DR   Araport; AT5G20420; -.
DR   TAIR; locus:2149957; AT5G20420.
DR   eggNOG; KOG0390; Eukaryota.
DR   HOGENOM; CLU_002499_0_0_1; -.
DR   InParanoid; F4K493; -.
DR   OMA; MELDQKF; -.
DR   OrthoDB; 64362at2759; -.
DR   PhylomeDB; F4K493; -.
DR   PRO; PR:F4K493; -.
DR   Proteomes; UP000006548; Chromosome 5.
DR   ExpressionAtlas; F4K493; baseline and differential.
DR   Genevisible; F4K493; AT.
DR   GO; GO:0005634; C:nucleus; IEA:UniProtKB-SubCell.
DR   GO; GO:0005524; F:ATP binding; IEA:UniProtKB-KW.
DR   GO; GO:0140658; F:ATP-dependent chromatin remodeler activity; IEA:InterPro.
DR   GO; GO:0004386; F:helicase activity; IEA:UniProtKB-KW.
DR   GO; GO:0016787; F:hydrolase activity; IEA:UniProtKB-KW.
DR   GO; GO:0080188; P:gene silencing by RNA-directed DNA methylation; IEA:InterPro.
DR   Gene3D; 3.40.50.10810; -; 1.
DR   Gene3D; 3.40.50.300; -; 1.
DR   InterPro; IPR044567; CLSY/DRD1.
DR   InterPro; IPR014001; Helicase_ATP-bd.
DR   InterPro; IPR001650; Helicase_C.
DR   InterPro; IPR027417; P-loop_NTPase.
DR   InterPro; IPR038718; SNF2-like_sf.
DR   InterPro; IPR000330; SNF2_N.
DR   PANTHER; PTHR45821; PTHR45821; 1.
DR   Pfam; PF00271; Helicase_C; 1.
DR   Pfam; PF00176; SNF2-rel_dom; 1.
DR   SMART; SM00487; DEXDc; 1.
DR   SMART; SM00490; HELICc; 1.
DR   SUPFAM; SSF52540; SSF52540; 2.
DR   PROSITE; PS51192; HELICASE_ATP_BIND_1; 1.
DR   PROSITE; PS51194; HELICASE_CTER; 1.
PE   1: Evidence at protein level;
KW   ATP-binding; Helicase; Hydrolase; Nucleotide-binding; Nucleus;
KW   Reference proteome.
FT   CHAIN           1..1261
FT                   /note="SNF2 domain-containing protein CLASSY 2"
FT                   /id="PRO_0000423314"
FT   DOMAIN          704..904
FT                   /note="Helicase ATP-binding"
FT                   /evidence="ECO:0000255|PROSITE-ProRule:PRU00541"
FT   DOMAIN          1067..1232
FT                   /note="Helicase C-terminal"
FT                   /evidence="ECO:0000255|PROSITE-ProRule:PRU00542"
FT   REGION          458..479
FT                   /note="Disordered"
FT                   /evidence="ECO:0000256|SAM:MobiDB-lite"
FT   MOTIF           855..858
FT                   /note="DEAH box"
FT   BINDING         717..724
FT                   /ligand="ATP"
FT                   /ligand_id="ChEBI:CHEBI:30616"
FT                   /evidence="ECO:0000255|PROSITE-ProRule:PRU00541"
SQ   SEQUENCE   1261 AA;  145314 MW;  B1C92FD74AF5E06D CRC64;
     MKKRGFYNLK HPFDPCPFEF FCSGTWKPVE YMRIEDGMMT IRLLENGYVL EDIRPFQRLR
     LRSRKAALSD CICFLRPDID VCVLYRIHED DLEPVWVDAR IVSIERKPHE SECSCKINVR
     IYIDQGCIGS EKQRINRDSV VIGLNQISIL QKFYKEQSTD QFYRWRFSED CTSLMKTRLS
     LGKFLPDLSW LTVTSTLKSI VFQIRTVQTK MVYQIVTDEE GSSSTLSSMN ITLEDGVSLS
     KVVKFNPADI LDDSQDLEIK QETDYYQEED EVVELRRSKR RNVRPDIYTG CDYEPDTIDG
     WVRMMPYQFG KCAVNVESDE DEDDNNEDGD TNDDLYIPLS RLFIKKKKTN SREAKPKSRK
     GEIVVIDKRR VHGFGRKERK SELSVIPFTP VFEPIPLEQF GLNANSFGGG GSFSRSQYFD
     ETEKYRSKGM KYGKKMTEME EMMEADLCWK GPNQVKSFQK RTSRSSRSVA PKTEDSDEPR
     VYKKVTLSAG AYNKLIDTYM NNIESTIAAK DEPTSVVDQW EELKKTNFAF KLHGDMEKNL
     SEDGEGETSE NEMLWREMEL CLASSYILDD NEVRVDNEAF EKARSGCEHD YRLEEEIGMC
     CRLCGHVGSE IKDVSAPFAE HKKWTIETKH IEEDDIKTKL SHKEAQTKDF SMISDSSEML
     AAEESDNVWA LIPKLKRKLH VHQRRAFEFL WRNVAGSVEP SLMDPTSGNI GGCVISHSPG
     AGKTFLIIAF LTSYLKLFPG KRPLVLAPKT TLYTWYKEFI KWEIPVPVHL IHGRRTYCTF
     KQNKTVQFNG VPKPSRDVMH VLDCLEKIQK WHAHPSVLVM GYTSFTTLMR EDSKFAHRKY
     MAKVLRESPG LLVLDEGHNP RSTKSRLRKA LMKVGTDLRI LLSGTLFQNN FCEYFNTLCL
     ARPKFIHEVL MELDQKFKTN HGVNKAPHLL ENRARKLFLD IIAKKIDASV GDERLQGLNM
     LKNMTNGFID NYEGSGSGSG DALPGLQIYT LVMNSTDIQH KILTKLQDVI KTYFGYPLEV
     ELQITLAAIH PWLVTSSNCC TKFFNPQELS EIGKLKHDAK KGSKVMFVLN LIFRVVKREK
     ILIFCHNIAP IRMFTELFEN IFRWQRGREI LTLTGDLELF ERGRVIDKFE EPGNPSRVLL
     ASITACAEGI SLTAASRVIM LDSEWNPSKT KQAIARAFRP GQQKVVYVYQ LLSRGTLEED
     KYRRTTWKEW VSCMIFSEEF VADPSLWQAE KIEDDILREI VGEDKVKSFH MIMKNEKAST
     G